chr14-26057684-T-C

Position:

• chr14-26057684-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.19 in 152,134 control chromosomes in the GnomAD database, including 2,825 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.19 (2825 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.270

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.221 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.26057684T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02306	ENST00000546412.2	n.258+68473A>G		intron_variant		3
LINC02306	ENST00000657312.1	n.458+68473A>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.190 AC: 28918 AN: 152016 Hom.: 2817 Cov.: 32

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.0811

Gnomad AMR AF: 0.187

Gnomad ASJ AF: 0.269

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.211

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.190 AC: 28955 AN: 152134 Hom.: 2825 Cov.: 32 AF XY: 0.187 AC XY: 13909 AN XY: 74388

Gnomad4 AFR AF: 0.225

Gnomad4 AMR AF: 0.187

Gnomad4 ASJ AF: 0.269

Gnomad4 EAS AF: 0.158

Gnomad4 SAS AF: 0.146

Gnomad4 FIN AF: 0.127

Gnomad4 NFE AF: 0.182

Gnomad4 OTH AF: 0.212

Alfa AF: 0.190 Hom.: 757

Bravo AF: 0.197

Asia WGS AF: 0.150 AC: 521 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.3
DANN	Benign	0.80

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs12433225; hg19: chr14-26526890;